Software for scientists

Proteomic and glycomic geekery

GlycoDomain Viewer

Further refinement of the GATOR tool, incorporating conserved domain
information, as well as information about post-translational modifications.
The tool is integrated with online spreadsheets, allowing for easy
overlay of your own data.

GATOR

Advanced web-app to present simply a wide variety of data from
proteomic data sources. Designed to work on a wide variety of
browsers, and be easy to use.

Sugar viewer/builder

Simple app/widget for drawing structures. Entirely vector-based,
using SVG to generate the images. This application currently is
dependent on a server-side component to run, but there's a
long-running project where it will be eventually moved across
to running in pure javascript on either the server or browser.

Sugarcore

Core classes written to manipulate carbohydrate structural data.
Primarily written to assist me in doing analysis during my PhD, it
was later enhanced to add the ability to generate composite
structures, which can be seen in the Sugar viewer/builder. While
this code largely works, it's not in a great state for anyone to
simply use.

GlycoSuite

Perl web-app actively maintained from 2001-2003. Unfortunately,
the source code for the application is not publicly available,
but it is still alive, and can be found hosted at Expasy.

MASCP-jstools

A toolkit for performing bioinformatic analysis on proteomic data
for Arabidopsis thaliana. Developed while at JBEI the software aggregates data from multiple
data sources and presents it all in an easy to use interface.
Even better, these same libraries can be taken from the web browser
and run from the command line, or on the server with little to no
modification of your code.

Phosphorylation / nsSNP

An analysis of the relationship between post-translational modifications and the rates of non-synonymous phosphorylation. In press.

Orthology map

Intricate map of how many proteins are shared between the golgi
proteomes of multiple species.